A5075887949- Genomics and Phylogenetic Studies
- Cassava research and cyanide
- Chromosomal and Genetic Variations
- Nematode management and characterization studies
- Banana Cultivation and Research
- Plant Pathogenic Bacteria Studies
- Genetic diversity and population structure
- Marine Ecology and Invasive Species
- Genetic and Environmental Crop Studies
- Environmental DNA in Biodiversity Studies
- Cocoa and Sweet Potato Agronomy
- Plant Virus Research Studies
- Genomics and Chromatin Dynamics
- Phytoplasmas and Hemiptera pathogens
- Methane Hydrates and Related Phenomena
- Amphibian and Reptile Biology
- Advanced Computational Techniques and Applications
- Seed and Plant Biochemistry
- Genetic and Clinical Aspects of Sex Determination and Chromosomal Abnormalities
- Marine Invertebrate Physiology and Ecology
- Solid-state spectroscopy and crystallography
- Forest ecology and management
- Physiological and biochemical adaptations
- Biofuel production and bioconversion
- T-cell and B-cell Immunology
University of California, Berkeley
2015-2025
Cassava (Manihot esculenta) provides calories and nutrition for more than half a billion people. It was domesticated by native Amazonian peoples through cultivation of the wild progenitor M. esculenta ssp. flabellifolia is now grown in tropical regions worldwide. Here we provide high-quality genome assembly cassava with improved contiguity, linkage, completeness; almost 97% genes are anchored to chromosomes. We find that paleotetraploidy shared related rubber tree Hevea, providing resource...
Acorn worms, also known as enteropneust (literally, 'gut-breathing') hemichordates, are marine invertebrates that share features with echinoderms and chordates. Together, these three phyla comprise the deuterostomes. Here we report draft genome sequences of two acorn Saccoglossus kowalevskii Ptychodera flava. By comparing them diverse bilaterian genomes, identify shared traits were probably inherited from last common deuterostome ancestor, then explore evolutionary trajectories leading this...
Abstract A central question in evolutionary biology is whether sponges or ctenophores (comb jellies) are the sister group to all other animals. These alternative phylogenetic hypotheses imply different scenarios for evolution of complex neural systems and animal-specific traits 1–6 . Conventional approaches based on morphological characters increasingly extensive gene sequence collections have not been able definitively answer this 7–11 Here we develop chromosome-scale linkage, also known as...
Cassava (Manihot esculenta Crantz) is an important staple food crop in Africa and South America; however, ubiquitous deleterious mutations may severely decrease its fitness. To evaluate these mutations, we constructed a cassava haplotype map through deep sequencing 241 diverse accessions identified >28 million segregating variants. We found that (i) although domestication has modified starch ketone metabolism pathways to allow for human consumption, the concomitant bottleneck clonal...
Animal genomes show networks of deeply conserved gene linkages whose phylogenetic scope and chromosomal context remain unclear. Here, we report chromosome-scale conservation synteny among bilaterians, cnidarians, sponges use comparative analysis to reconstruct ancestral chromosomes across major animal groups. Comparisons diverse metazoans reveal the processes chromosome evolution that produced contemporary karyotypes from their Precambrian progenitors. On basis these findings, introduce a...
Abstract Frogs are an ecologically diverse and phylogenetically ancient group of anuran amphibians that include important vertebrate cell developmental model systems, notably the genus Xenopus . Here we report a high-quality reference genome sequence for western clawed frog, tropicalis , along with draft chromosome-scale sequences three distantly related emerging frog species, Eleutherodactylus coqui Engystomops pustulosus Hymenochirus boettgeri Frog chromosomes have remained remarkably...
Abstract Miscanthus is a perennial wild grass that of global importance for paper production, roofing, horticultural plantings, and an emerging highly productive temperate biomass crop. We report chromosome-scale assembly the paleotetraploid M. sinensis genome, providing resource links its chromosomes to related diploid Sorghum complex polyploid sugarcanes. The asymmetric distribution transposons across two homoeologous subgenomes proves paleo-allotetraploidy identifies several balanced...
SUMMARY Trifoliate orange ( Poncirus trifoliata ), a deciduous close relative of evergreen Citrus , has important traits for citrus production, including tolerance/resistance to greening disease (Huanglongbing, HLB) and other major diseases, cold tolerance. It been one the most rootstocks, valuable sources resistance tolerance genes citrus. Here we present high‐quality, chromosome‐scale genome assembly P. . The 264.9‐Mb contains nine chromosomal pseudomolecules with 25 538 protein‐coding...
The nutrient-rich tubers of the greater yam, Dioscorea alata L., provide food and income security for millions people around world. Despite its global importance, however, yam remains an orphan crop. Here, we address this resource gap by presenting a highly contiguous chromosome-scale genome assembly D. combined with dense genetic map derived from African breeding populations. sequence reveals ancient allotetraploidization in lineage, followed extensive genome-wide reorganization. Using...
Genetic mapping of quantitative trait loci (QTL) for resistance to cassava brown streak disease (CBSD), mosaic (CMD) and green mite (CGM) was performed using an F1 cross developed between the Tanzanian landrace, Kiroba, a breeding line, AR37-80. The population evaluated two consecutive years in sites Tanzania. A genetic linkage map derived from 106 progeny 1974 SNP markers spanned 18 chromosomes covering distance 1698 cM. Thirteen significant QTL were identified; three are associated with...
Bill and Melinda Gates Foundation (BMGF) Grant OPPGD1493. University of Arizona. CGIAR Research Program on Roots, Tubers, Bananas. Next Generation Cassava Breeding grant OPP1048542 from BMGF the United Kingdom Department for International Development. OPPGD1016 to IITA. National Institutes Health S10 Instrumentation Grants S10RR029668 S10RR027303.
Abstract Closely related muntjac deer show striking karyotype differences. Here we describe chromosome-scale genome assemblies for Chinese and Indian muntjacs, Muntiacus reevesi (2 n = 46) muntjak vaginalis 6/7), analyze their evolution architecture. The genomes extensive collinearity with each other cattle. We identified numerous fusion events unique to shared by muntjacs relative the cervid ancestor, confirming many cytogenetic observations sequence. One of these M. fusions reversed an...
QTL consistent across seasons were detected for resistance to cassava brown streak disease induced root necrosis and foliar symptoms. The CMD2 locus was in an East African landrace, comprised two QTL. Cassava production Africa is compromised by (CBSD) mosaic (CMD). To reduce costs increase the precision of breeding, a study conducted identify molecular markers linked against these diseases. A bi-parental F1 mapping population developed from cross between Tanzanian farmer varieties, Namikonga...
ABSTRACT Identifying populations at highest risk from climate change is a critical component of conservation efforts. However, vulnerability assessments are usually applied the species level, even though intraspecific variation in exposure, sensitivity and adaptive capacity play crucial role determining vulnerability. Genomic data can inform by identifying signatures local adaptation that reflect population‐level capacity. Here, we address question to temperature genetic basis thermal...
In many groups, sex chromosomes change frequently but the drivers of their rapid evolution are varied and often poorly characterized. With an aim further understanding chromosome turnover, we investigated polymorphic Marsabit clawed frog, Xenopus borealis, using genomic data a new chromosome-scale genome assembly. We confirmed previous findings that 54.1 Mb 8L is sex-linked in animals from east Kenya laboratory strain, most (or all) this region not natural populations west Kenya. Previous...
In Sub-Saharan Africa cassava (Manihot esculenta Crantz) is one of the most important food crops where more than 40% population relies on it as their staple carbohydrate source. Biotic constraints such viral diseases, mainly Cassava Mosaic Disease (CMD) and Brown Streak (CBSD), arthropod pests, particularly Green Mite (CGM), are major to realization cassava's full production potential in Africa. To address these problems, we aimed map quantitative trait loci (QTL) associated with resistance...
Abstract Frogs are an ecologically diverse and phylogenetically ancient group of living amphibians that include important vertebrate cell developmental model systems, notably the genus Xenopus . Here we report a high-quality reference genome sequence for western clawed frog, tropicalis , along with draft chromosome-scale sequences three distantly related emerging frog species, Eleutherodactylus coqui Engystomops pustulosus Hymenochirus boettgeri Frog chromosomes have remained remarkably...
Abstract The nutrient-rich tubers of the greater yam Dioscorea alata L. provide food and income security for millions people around world. Despite its global importance, however, remains an “orphan crop.” Here we address this resource gap by presenting a highly-contiguous chromosome-scale genome assembly combined with dense genetic map derived from African breeding populations. sequence reveals ancient lineage-specific duplication, followed extensive genome-wide reorganization. Using our new...
Emerging research organisms enable the study of biology that cannot be addressed using classical 'model' organisms. New data resources can accelerate in such animals. Here, we present new functional genomic for amphipod crustacean Parhyale hawaiensis, facilitating exploration gene regulatory evolution this emerging organism. We use Omni-ATAC-seq to identify accessible chromatin genome-wide across a broad time course embryonic development. This encompasses many major morphological events,...
Cassava (Manihot esculenta Crantz) is a food and industrial storage root crop with substantial potential to contribute managing risk associated climate change due its inherent resilience in providing biodegradable option manufacturing. In Africa, cassava production challenged by two viral diseases, brown streak disease (CBSD) mosaic disease. Here we detect quantitative trait loci (QTL) CBSD biparental mapping population of Tanzanian landrace, Nachinyaya AR37-80, phenotyped locations over...
Cassava ( Manihot esculenta Crantz) is an important staple food crop in Africa and South America, however, ubiquitous deleterious mutations may severely reduce its fitness. To evaluate these the cassava genome, we constructed a haplotype map using deep sequencing from 241 diverse accessions identified over 28 million segregating variants. We found that, 1) while domestication modified starch ketone metabolism pathways for human consumption, concomitant bottleneck clonal propagation resulted...
Abstract Despite their recent divergence, muntjac deer show striking karyotype differences. Here we describe new chromosome-scale genome assemblies for the Chinese and Indian muntjacs, Muntiacus reevesi (2n=46) muntjak (2n=6/7), analyze evolution architecture. We identified six fusion events shared by both species relative to cervid ancestor therefore present in common ancestor, unique M. lineage, twenty-six lineage. One of these fusions reverses an earlier fission Although comparative Hi-C...